Provide hard filtering for indels when initial VQSR fails only on indels
Merge
Fix bug in test_pipeline.py relating to change in programs._get_versions() name
Merge pull request #7 from mariogiov/fix_test_pipeline

Fix bug in test_pipeline.py relating to change in programs._get_versions...
Merge pull request #99 from mariogiov/fix_test_pipeline

Fix bug in test_pipeline.py relating to change in programs._get_versions...
Merge pull request #8 from chapmanb/master

Merge from Brad upstream
Changed pipeline/config_utils.py to expand shell variables into paths (specifically for snpEff)
Custom filtering of FreeBayes with bcbio.variation, falling back on standard hard filters
Merge pull request #101 from mariogiov/master

Expand shell variables into paths in config_utils.py
Update Miniconda download to latest released version. Fixes #100
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Use bash shell and pipefail for piped commands to provide better detection of errors during alignment steps. #103
Ensure picard memory options used over gatk if present in resources. Continue to default to GATK if not specified
Ensure QC runs after BAM merging so full files available for summary reports. Thanks to Zhengqiu Cai
Handle checking for VQSR when not doing variant calling
Fixes for single end RNA-seq analysis. Thanks to Shannan Ho Sui
Provide a way to check MuTect's version. However due to an issue,
it reports the GATK version it is based on instead: until this is
fixed, we use a hack knowing that 1.1.4 is based on GATK 2.2 and
1.1.5 on GATK 2.7.
Ensure that only MuTect 1.1.5 or higher is allowed to run
Remove hack for MuTect errors, not needed anymore with 1.1.5
fixed positional argument passing bug (affected at least bowtie2 calls)